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Member "augustus-3.3.3/docs/tutorial-cgp/data/augCGP_rnaseq/joined_pred/rheMac3.gff" (22 May 2019, 13075 Bytes) of package /linux/misc/augustus-3.3.3.tar.gz:


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    1 # overlap start --------------------------------------------------------------------------------
    2 # this overlap has 1 different transcripts
    3 # This transcript jg1.t1 is derived from g1.t1 from the input file pred1/rheMac3.cgp.gff
    4 # It is supported by 1 other predicted genes
    5 # the core of this joined transcript has priority 1
    6 chr20	AUGUSTUS	transcript	1	45360	.	-	.	jg1.t1
    7 chr20	AUGUSTUS	tts	1	1	.	-	.	transcript_id "jg1.t1"; gene_id "jg1";
    8 chr20	AUGUSTUS	UTR	1	1901	0	-	.	transcript_id "jg1.t1"; gene_id "jg1";
    9 chr20	AUGUSTUS	stop_codon	1902	1904	.	-	0	transcript_id "jg1.t1"; gene_id "jg1";
   10 chr20	AUGUSTUS	CDS	1902	2043	1	-	1	transcript_id "jg1.t1"; gene_id "jg1";
   11 chr20	AUGUSTUS	CDS	2662	2829	1	-	1	transcript_id "jg1.t1"; gene_id "jg1";
   12 chr20	AUGUSTUS	CDS	3240	3269	1	-	1	transcript_id "jg1.t1"; gene_id "jg1";
   13 chr20	AUGUSTUS	CDS	6126	6214	1	-	0	transcript_id "jg1.t1"; gene_id "jg1";
   14 chr20	AUGUSTUS	CDS	13361	13537	1	-	0	transcript_id "jg1.t1"; gene_id "jg1";
   15 chr20	AUGUSTUS	CDS	19968	20111	1	-	0	transcript_id "jg1.t1"; gene_id "jg1";
   16 chr20	AUGUSTUS	CDS	22184	22294	0	-	0	transcript_id "jg1.t1"; gene_id "jg1";
   17 chr20	AUGUSTUS	CDS	35057	35155	0	-	0	transcript_id "jg1.t1"; gene_id "jg1";
   18 chr20	AUGUSTUS	CDS	43271	43365	0	-	2	transcript_id "jg1.t1"; gene_id "jg1";
   19 chr20	AUGUSTUS	CDS	45300	45360	0	-	0	transcript_id "jg1.t1"; gene_id "jg1";
   20 chr20	AUGUSTUS	start_codon	45358	45360	.	-	0	transcript_id "jg1.t1"; gene_id "jg1";
   21 # overlap start --------------------------------------------------------------------------------
   22 # this overlap has 1 different transcripts
   23 # This transcript jg2.t1 is derived from g2.t1 from the input file pred6/rheMac3.cgp.gff
   24 # It is supported by 0 other predicted genes
   25 # the core of this joined transcript has priority 1
   26 chr20	AUGUSTUS	transcript	54177	72866	.	+	.	jg2.t1
   27 chr20	AUGUSTUS	start_codon	54177	54179	.	+	0	transcript_id "jg2.t1"; gene_id "jg2";
   28 chr20	AUGUSTUS	CDS	54177	54267	1	+	0	transcript_id "jg2.t1"; gene_id "jg2";
   29 chr20	AUGUSTUS	CDS	69008	69129	1	+	2	transcript_id "jg2.t1"; gene_id "jg2";
   30 chr20	AUGUSTUS	CDS	72864	72866	1	+	0	transcript_id "jg2.t1"; gene_id "jg2";
   31 chr20	AUGUSTUS	stop_codon	72864	72866	.	+	0	transcript_id "jg2.t1"; gene_id "jg2";
   32 # overlap start --------------------------------------------------------------------------------
   33 # this overlap has 1 different transcripts
   34 # This transcript jg3.t1 is derived from g1.t1 from the input file pred7/rheMac3.cgp.gff
   35 # It is supported by 1 other predicted genes
   36 # the core of this joined transcript has priority 1
   37 chr20	AUGUSTUS	transcript	54142	87146	.	+	.	jg3.t1
   38 chr20	AUGUSTUS	tss	54142	54142	.	+	.	transcript_id "jg3.t1"; gene_id "jg3";
   39 chr20	AUGUSTUS	UTR	54142	54267	0	+	.	transcript_id "jg3.t1"; gene_id "jg3";
   40 chr20	AUGUSTUS	UTR	69008	69129	0	+	.	transcript_id "jg3.t1"; gene_id "jg3";
   41 chr20	AUGUSTUS	UTR	72864	72896	0	+	.	transcript_id "jg3.t1"; gene_id "jg3";
   42 chr20	AUGUSTUS	start_codon	72897	72899	.	+	0	transcript_id "jg3.t1"; gene_id "jg3";
   43 chr20	AUGUSTUS	CDS	72897	73164	0.54	+	0	transcript_id "jg3.t1"; gene_id "jg3";
   44 chr20	AUGUSTUS	CDS	81009	81125	1	+	2	transcript_id "jg3.t1"; gene_id "jg3";
   45 chr20	AUGUSTUS	CDS	81500	81691	1	+	2	transcript_id "jg3.t1"; gene_id "jg3";
   46 chr20	AUGUSTUS	CDS	82873	83003	1	+	2	transcript_id "jg3.t1"; gene_id "jg3";
   47 chr20	AUGUSTUS	CDS	83478	83610	1	+	0	transcript_id "jg3.t1"; gene_id "jg3";
   48 chr20	AUGUSTUS	CDS	83805	83934	1	+	2	transcript_id "jg3.t1"; gene_id "jg3";
   49 chr20	AUGUSTUS	CDS	84326	84466	1	+	1	transcript_id "jg3.t1"; gene_id "jg3";
   50 chr20	AUGUSTUS	CDS	84760	84835	1	+	1	transcript_id "jg3.t1"; gene_id "jg3";
   51 chr20	AUGUSTUS	CDS	85068	85223	1	+	0	transcript_id "jg3.t1"; gene_id "jg3";
   52 chr20	AUGUSTUS	CDS	85669	85771	1	+	0	transcript_id "jg3.t1"; gene_id "jg3";
   53 chr20	AUGUSTUS	CDS	85866	86077	1	+	2	transcript_id "jg3.t1"; gene_id "jg3";
   54 chr20	AUGUSTUS	stop_codon	86075	86077	.	+	0	transcript_id "jg3.t1"; gene_id "jg3";
   55 chr20	AUGUSTUS	UTR	86078	87146	0	+	.	transcript_id "jg3.t1"; gene_id "jg3";
   56 chr20	AUGUSTUS	tts	87146	87146	.	+	.	transcript_id "jg3.t1"; gene_id "jg3";
   57 # overlap start --------------------------------------------------------------------------------
   58 # this overlap has 1 different transcripts
   59 # This transcript jg4.t1 is derived from g2.t1 from the input file pred8/rheMac3.cgp.gff
   60 # It is supported by 1 other predicted genes
   61 # the core of this joined transcript has priority 1
   62 chr20	AUGUSTUS	transcript	88892	102432	.	-	.	jg4.t1
   63 chr20	AUGUSTUS	tts	88892	88892	.	-	.	transcript_id "jg4.t1"; gene_id "jg4";
   64 chr20	AUGUSTUS	UTR	88892	90161	0	-	.	transcript_id "jg4.t1"; gene_id "jg4";
   65 chr20	AUGUSTUS	stop_codon	90162	90164	.	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   66 chr20	AUGUSTUS	CDS	90162	90276	1	-	1	transcript_id "jg4.t1"; gene_id "jg4";
   67 chr20	AUGUSTUS	CDS	90396	90478	1	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   68 chr20	AUGUSTUS	CDS	92556	92694	1	-	1	transcript_id "jg4.t1"; gene_id "jg4";
   69 chr20	AUGUSTUS	CDS	92777	92864	1	-	2	transcript_id "jg4.t1"; gene_id "jg4";
   70 chr20	AUGUSTUS	CDS	93043	93158	1	-	1	transcript_id "jg4.t1"; gene_id "jg4";
   71 chr20	AUGUSTUS	CDS	93252	93365	1	-	1	transcript_id "jg4.t1"; gene_id "jg4";
   72 chr20	AUGUSTUS	CDS	93458	93519	1	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   73 chr20	AUGUSTUS	CDS	93599	93628	0.21	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   74 chr20	AUGUSTUS	CDS	94961	95029	0	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   75 chr20	AUGUSTUS	CDS	95574	95655	0	-	1	transcript_id "jg4.t1"; gene_id "jg4";
   76 chr20	AUGUSTUS	CDS	95842	95918	0.97	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   77 chr20	AUGUSTUS	CDS	96122	96180	0	-	2	transcript_id "jg4.t1"; gene_id "jg4";
   78 chr20	AUGUSTUS	CDS	96293	96344	0	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   79 chr20	AUGUSTUS	CDS	97055	97161	0	-	2	transcript_id "jg4.t1"; gene_id "jg4";
   80 chr20	AUGUSTUS	CDS	97356	97406	0	-	2	transcript_id "jg4.t1"; gene_id "jg4";
   81 chr20	AUGUSTUS	CDS	102315	102432	0	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   82 chr20	AUGUSTUS	start_codon	102430	102432	.	-	0	transcript_id "jg4.t1"; gene_id "jg4";
   83 # overlap start --------------------------------------------------------------------------------
   84 # this overlap has 1 different transcripts
   85 # This transcript jg5.t1 is derived from g3.t1 from the input file pred8/rheMac3.cgp.gff
   86 # It is supported by 1 other predicted genes
   87 # the core of this joined transcript has priority 1
   88 chr20	AUGUSTUS	transcript	104514	107444	.	+	.	jg5.t1
   89 chr20	AUGUSTUS	start_codon	104514	104516	.	+	0	transcript_id "jg5.t1"; gene_id "jg5";
   90 chr20	AUGUSTUS	CDS	104514	105147	0	+	0	transcript_id "jg5.t1"; gene_id "jg5";
   91 chr20	AUGUSTUS	CDS	105741	105920	0	+	2	transcript_id "jg5.t1"; gene_id "jg5";
   92 chr20	AUGUSTUS	CDS	106023	106106	0	+	2	transcript_id "jg5.t1"; gene_id "jg5";
   93 chr20	AUGUSTUS	CDS	106283	106359	1	+	2	transcript_id "jg5.t1"; gene_id "jg5";
   94 chr20	AUGUSTUS	CDS	107112	107264	0.99	+	0	transcript_id "jg5.t1"; gene_id "jg5";
   95 chr20	AUGUSTUS	stop_codon	107262	107264	.	+	0	transcript_id "jg5.t1"; gene_id "jg5";
   96 chr20	AUGUSTUS	UTR	107265	107444	0	+	.	transcript_id "jg5.t1"; gene_id "jg5";
   97 chr20	AUGUSTUS	tts	107444	107444	.	+	.	transcript_id "jg5.t1"; gene_id "jg5";
   98 # overlap start --------------------------------------------------------------------------------
   99 # this overlap has 1 different transcripts
  100 # This transcript jg6.t1 is derived from g4.t1 from the input file pred8/rheMac3.cgp.gff
  101 # It is supported by 1 other predicted genes
  102 # the core of this joined transcript has priority 1
  103 chr20	AUGUSTUS	transcript	107598	111253	.	+	.	jg6.t1
  104 chr20	AUGUSTUS	start_codon	107598	107600	.	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  105 chr20	AUGUSTUS	CDS	107598	107793	1	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  106 chr20	AUGUSTUS	CDS	108785	108991	1	+	2	transcript_id "jg6.t1"; gene_id "jg6";
  107 chr20	AUGUSTUS	CDS	109057	109190	1	+	2	transcript_id "jg6.t1"; gene_id "jg6";
  108 chr20	AUGUSTUS	CDS	109272	109409	0.85	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  109 chr20	AUGUSTUS	CDS	109478	109594	1	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  110 chr20	AUGUSTUS	CDS	109706	109831	0.94	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  111 chr20	AUGUSTUS	CDS	109938	110135	1	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  112 chr20	AUGUSTUS	CDS	110391	110511	1	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  113 chr20	AUGUSTUS	CDS	110592	110773	0.99	+	2	transcript_id "jg6.t1"; gene_id "jg6";
  114 chr20	AUGUSTUS	CDS	110870	110980	0.98	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  115 chr20	AUGUSTUS	CDS	111103	111147	1	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  116 chr20	AUGUSTUS	stop_codon	111145	111147	.	+	0	transcript_id "jg6.t1"; gene_id "jg6";
  117 chr20	AUGUSTUS	UTR	111148	111253	0	+	.	transcript_id "jg6.t1"; gene_id "jg6";
  118 chr20	AUGUSTUS	tts	111253	111253	.	+	.	transcript_id "jg6.t1"; gene_id "jg6";
  119 # overlap start --------------------------------------------------------------------------------
  120 # this overlap has 1 different transcripts
  121 # This transcript jg7.t1 is derived from g2.t1 from the input file pred2/rheMac3.cgp.gff
  122 # It is supported by 1 other predicted genes
  123 # the core of this joined transcript has priority 1
  124 # transcrpit has been joined at 5'-side with g1.t1
  125 chr20	AUGUSTUS	transcript	111468	180501	.	-	.	jg7.t1
  126 chr20	AUGUSTUS	tts	111468	111468	.	-	.	transcript_id "jg7.t1"; gene_id "jg7";
  127 chr20	AUGUSTUS	UTR	111468	112133	0	-	.	transcript_id "jg7.t1"; gene_id "jg7";
  128 chr20	AUGUSTUS	stop_codon	112134	112136	.	-	0	transcript_id "jg7.t1"; gene_id "jg7";
  129 chr20	AUGUSTUS	CDS	112134	112260	1	-	1	transcript_id "jg7.t1"; gene_id "jg7";
  130 chr20	AUGUSTUS	CDS	113467	113634	1	-	1	transcript_id "jg7.t1"; gene_id "jg7";
  131 chr20	AUGUSTUS	CDS	115179	115286	0	-	1	transcript_id "jg7.t1"; gene_id "jg7";
  132 chr20	AUGUSTUS	CDS	117333	117578	0	-	1	transcript_id "jg7.t1"; gene_id "jg7";
  133 chr20	AUGUSTUS	CDS	121067	121237	1	-	1	transcript_id "jg7.t1"; gene_id "jg7";
  134 chr20	AUGUSTUS	CDS	121645	122174	0	-	0	transcript_id "jg7.t1"; gene_id "jg7";
  135 chr20	AUGUSTUS	CDS	129055	129192	0.86	-	0	transcript_id "jg7.t1"; gene_id "jg7";
  136 chr20	AUGUSTUS	CDS	135293	135389	1	-	1	transcript_id "jg7.t1"; gene_id "jg7";
  137 chr20	AUGUSTUS	CDS	139001	139141	1	-	1	transcript_id "jg7.t1"; gene_id "jg7";
  138 chr20	AUGUSTUS	CDS	175212	176089	1	-	0	transcript_id "jg7.t1"; gene_id "jg7";
  139 chr20	AUGUSTUS	start_codon	176087	176089	.	-	0	transcript_id "jg7.t1"; gene_id "jg7";
  140 chr20	AUGUSTUS	UTR	176090	176170	0	-	.	transcript_id "jg7.t1"; gene_id "jg7";
  141 chr20	AUGUSTUS	UTR	180270	180501	0	-	.	transcript_id "jg7.t1"; gene_id "jg7";
  142 chr20	AUGUSTUS	tss	180501	180501	.	-	.	transcript_id "jg7.t1"; gene_id "jg7";
  143 # overlap start --------------------------------------------------------------------------------
  144 # this overlap has 1 different transcripts
  145 # This transcript jg8.t1 is derived from g1.t1 from the input file pred5/rheMac3.cgp.gff
  146 # It is supported by 1 other predicted genes
  147 # the core of this joined transcript has priority 1
  148 chr20	AUGUSTUS	transcript	194467	198926	.	-	.	jg8.t1
  149 chr20	AUGUSTUS	tts	194467	194467	.	-	.	transcript_id "jg8.t1"; gene_id "jg8";
  150 chr20	AUGUSTUS	UTR	194467	194753	0	-	.	transcript_id "jg8.t1"; gene_id "jg8";
  151 chr20	AUGUSTUS	stop_codon	194754	194756	.	-	0	transcript_id "jg8.t1"; gene_id "jg8";
  152 chr20	AUGUSTUS	CDS	194754	194861	1	-	0	transcript_id "jg8.t1"; gene_id "jg8";
  153 chr20	AUGUSTUS	CDS	195400	195486	1	-	0	transcript_id "jg8.t1"; gene_id "jg8";
  154 chr20	AUGUSTUS	CDS	195573	195707	1	-	0	transcript_id "jg8.t1"; gene_id "jg8";
  155 chr20	AUGUSTUS	CDS	196134	196286	0	-	0	transcript_id "jg8.t1"; gene_id "jg8";
  156 chr20	AUGUSTUS	CDS	198666	198926	0	-	0	transcript_id "jg8.t1"; gene_id "jg8";
  157 chr20	AUGUSTUS	start_codon	198924	198926	.	-	0	transcript_id "jg8.t1"; gene_id "jg8";
  158 # overlap start --------------------------------------------------------------------------------
  159 # this overlap has 1 different transcripts
  160 # This transcript jg9.t1 is derived from g2.t1 from the input file pred5/rheMac3.cgp.gff
  161 # It is supported by 1 other predicted genes
  162 # the core of this joined transcript has priority 1
  163 chr20	AUGUSTUS	transcript	199312	205304	.	-	.	jg9.t1
  164 chr20	AUGUSTUS	stop_codon	199312	199314	.	-	0	transcript_id "jg9.t1"; gene_id "jg9";
  165 chr20	AUGUSTUS	CDS	199312	199608	1	-	0	transcript_id "jg9.t1"; gene_id "jg9";
  166 chr20	AUGUSTUS	CDS	199932	200048	1	-	0	transcript_id "jg9.t1"; gene_id "jg9";
  167 chr20	AUGUSTUS	CDS	201331	201477	1	-	0	transcript_id "jg9.t1"; gene_id "jg9";
  168 chr20	AUGUSTUS	CDS	201537	201715	1	-	2	transcript_id "jg9.t1"; gene_id "jg9";
  169 chr20	AUGUSTUS	CDS	202070	202206	1	-	1	transcript_id "jg9.t1"; gene_id "jg9";
  170 chr20	AUGUSTUS	CDS	202446	202569	1	-	2	transcript_id "jg9.t1"; gene_id "jg9";
  171 chr20	AUGUSTUS	CDS	202657	202747	1	-	0	transcript_id "jg9.t1"; gene_id "jg9";
  172 chr20	AUGUSTUS	CDS	203436	203755	1	-	2	transcript_id "jg9.t1"; gene_id "jg9";
  173 chr20	AUGUSTUS	CDS	203844	204112	1	-	1	transcript_id "jg9.t1"; gene_id "jg9";
  174 chr20	AUGUSTUS	CDS	204307	204434	1	-	0	transcript_id "jg9.t1"; gene_id "jg9";
  175 chr20	AUGUSTUS	CDS	204648	204855	1	-	1	transcript_id "jg9.t1"; gene_id "jg9";
  176 chr20	AUGUSTUS	CDS	204940	205117	1	-	2	transcript_id "jg9.t1"; gene_id "jg9";
  177 chr20	AUGUSTUS	CDS	205226	205304	0.52	-	0	transcript_id "jg9.t1"; gene_id "jg9";
  178 chr20	AUGUSTUS	start_codon	205302	205304	.	-	0	transcript_id "jg9.t1"; gene_id "jg9";